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Published April 15, 2021 | Version v4.32
Software Open

Clinical-Genomics/scout: MITOMAP annotations support, Splice Junction Tracks and maintenance

Authors/Creators

  • 1. Clinical Genomics, Science for Life Laboratory,
  • 2. Science for Life Labs
  • 3. @Futurice
  • 4. @Clinical-Genomics
  • 5. Karolinska Institutet, Genomic Medicine Sweden
  • 6. Unemployed for the moment
  • 7. SciLifeLab, @Clinical-Genomics

Description

[4.32] Added
  • Load and show MITOMAP associated diseases from VCF (INFO field: MitomapAssociatedDiseases, via HmtNote)
  • Show variant allele frequencies for mitochondrial variants (GRCh38 cases)
  • Extend "public" json API with diseases (OMIM) and phenotypes (HPO)
  • HPO gene list download now has option for clinical and non-clinical genes
  • Display gene splice junctions data in sashimi plots
  • Update case individuals with splice junctions tracks
  • Simple Docker compose for development with local build
  • Make Phenomodels subpanels collapsible
  • User side documentation of cytogenomics features (Gens, Chromograph, vcf2cytosure, rhocall)
  • iSort GitHub Action ### Fixed
  • Show other causative once, even if several events point to it
  • Filtering variants by mitochondrial chromosome for cases with genome build=38
  • HPO gene search button triggers any warnings for clinical / non-existing genes also on first search
  • Fixed a bug in variants pages caused by MT variants without alt_frequency
  • Tests for CADD score parsing function
  • Fixed the look of IGV settings on SNV variant page
  • Cases analyzed once shown as rerun
  • Missing case track on case re-upload
  • Fixed severity rank for SO term "regulatory region ablation" ### Changed
  • Refactor according to CodeFactor - mostly reuse of duplicated code
  • Phenomodels language adjustment
  • Open variants in a new window (from variants page)
  • Open overlapping and compound variants in a new window (from variant page)
  • gnomAD link points to gnomAD v.3 (build GRCh38) for mitochondrial variants.
  • Display only number of affected genes for dismissed SVs in general report
  • Chromosome build check when populating the variants filter chromosome selection
  • Display mitochondrial and rare diseases coverage report in cases with missing 'rare' track

Files

Clinical-Genomics/scout-v4.32.zip

Files (15.2 MB)

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md5:98d4d83122c9d3a712b8d3a2b65eefb0
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Additional details

Related works

Is supplement to
https://github.com/Clinical-Genomics/scout/tree/v4.32 (URL)